I did this on my 40B. I took longer then expected and lost fish. I had them in a 5gal. Wasnt so much the bacteria thing as I transfered the filter media as I think it was the stress associated with the extended time for the transfer. Weird thing was all my neon tetras lived, 3 out of 4 of my false jullies, and the betta did ok. The two mollies and two green cories and 1 false julie didnt make it. I personally thought it would have been the other way around as the mollies and green cories were healthier looking.
Anyhow if you have another tank to throw them in while you do the change over I highly recommend it. Just my amateur input.